HEADER RIBOSOMAL PROTEIN 23-JUL-10 3IYY TITLE COORDINATES OF THE B1B BRIDGE-FORMING PROTEIN STRUCTURES FITTED INTO TITLE 2 THE CRYO-EM MAP OF EFG.GDPNP-BOUND E.COLI 70S RIBOSOME(EMD-1363) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 50S RIBOSOMAL PROTEIN L31; COMPND 3 CHAIN: A; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: 50S RIBOSOMAL PROTEIN L5; COMPND 6 CHAIN: F; COMPND 7 MOL_ID: 3; COMPND 8 MOLECULE: 30S RIBOSOMAL PROTEIN S13; COMPND 9 CHAIN: M SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 701177; SOURCE 4 STRAIN: MRE600; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 7 ORGANISM_TAXID: 701177; SOURCE 8 MOL_ID: 3; SOURCE 9 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 10 ORGANISM_TAXID: 701177 KEYWDS RIBOSOMAL INTERSUBUNIT BRIDGES, B1B BRIDGE, RATCHET-LIKE MOTION, KEYWDS 2 RIBOSOMAL PROTEIN L31, RIBOSOMAL PROTEIN EXPDTA ELECTRON MICROSCOPY MDLTYP CA ATOMS ONLY, CHAIN A, F, M AUTHOR M.SHASMAL,B.CHAKRABORTY,J.SENGUPTA REVDAT 4 21-FEB-24 3IYY 1 REMARK REVDAT 3 18-DEC-19 3IYY 1 CRYST1 SCALE REVDAT 2 18-JUL-18 3IYY 1 REMARK REVDAT 1 01-SEP-10 3IYY 0 JRNL AUTH M.SHASMAL,B.CHAKRABORTY,J.SENGUPTA JRNL TITL INTRINSIC MOLECULAR PROPERTIES OF THE PROTEIN-PROTEIN BRIDGE JRNL TITL 2 FACILITATE RATCHET-LIKE MOTION OF THE RIBOSOME. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 399 192 2010 JRNL REFN ISSN 0006-291X JRNL PMID 20643101 JRNL DOI 10.1016/J.BBRC.2010.07.053 REMARK 2 REMARK 2 RESOLUTION. 10.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : SPIDER REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 2AW7 REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : 2.820 REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 10.90 REMARK 3 NUMBER OF PARTICLES : NULL REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 3IYY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000160040. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : VITREOUS ICE (CRYO EM) REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : E.COLI 70S RIBOSOME REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : QUANTIFOIL HOLLEY CARBON FILM REMARK 245 GRIDS REMARK 245 SAMPLE VITRIFICATION DETAILS : RAPID-FREEZING IN LIQUID ETHANE REMARK 245 SAMPLE BUFFER : POLYMIX BUFFER REMARK 245 PH : NULL REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 11-JUL-03 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : 93.00 REMARK 245 MICROSCOPE MODEL : FEI TECNAI F20 REMARK 245 DETECTOR TYPE : KODAK SO-163 FILM REMARK 245 MINIMUM DEFOCUS (NM) : 2000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 4000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 NOMINAL CS : 2.00 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 2000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 50000 REMARK 245 CALIBRATED MAGNIFICATION : 49696 REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, F, M REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET F 0 REMARK 465 MET M 0 REMARK 465 PRO M 114 REMARK 465 ILE M 115 REMARK 465 LYS M 116 REMARK 465 LYS M 117 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2AW7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI 30S RIBOSOME AT 3.5 A REMARK 900 RESOLUTION CHAIN M: SMALL SUBUNIT PROTEIN S13 REMARK 900 RELATED ID: 2AWB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI 50S RIBOSOME AT 3.5 A REMARK 900 RESOLUTION CHAIN F: LARGE SUBUNIT PROTEIN L5 REMARK 900 RELATED ID: 2WRJ RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF THE T. THERMOPHILUS 70S RIBOSOME (CHAIN 4 WAS REMARK 900 USED AS TEMPLATE TO BUILD HOMOLOGY MODEL OF E.COLI L31) REMARK 900 RELATED ID: EMD-1363 RELATED DB: EMDB REMARK 900 CRYO-EM MAP OF EF-G BOUND RELEASE COMPLEX OF E. COLI IN THE REMARK 900 PRESENCE OF PUROMYCIN AND GDPNP DBREF 3IYY A 1 70 UNP D3QYD6 D3QYD6_ECOCB 1 70 DBREF 3IYY F 0 178 UNP D3QTE7 D3QTE7_ECOCB 1 179 DBREF 3IYY M 0 117 UNP D3QTD7 D3QTD7_ECOCB 1 118 SEQRES 1 A 70 MET LYS LYS ASP ILE HIS PRO LYS TYR GLU GLU ILE THR SEQRES 2 A 70 ALA SER CYS SER CYS GLY ASN VAL MET LYS ILE ARG SER SEQRES 3 A 70 THR VAL GLY HIS ASP LEU ASN LEU ASP VAL CYS SER LYS SEQRES 4 A 70 CYS HIS PRO PHE PHE THR GLY LYS GLN ARG ASP VAL ALA SEQRES 5 A 70 THR GLY GLY ARG VAL ASP ARG PHE ASN LYS ARG PHE ASN SEQRES 6 A 70 ILE PRO GLY SER LYS SEQRES 1 F 179 MET ALA LYS LEU HIS ASP TYR TYR LYS ASP GLU VAL VAL SEQRES 2 F 179 LYS LYS LEU MET THR GLU PHE ASN TYR ASN SER VAL MET SEQRES 3 F 179 GLN VAL PRO ARG VAL GLU LYS ILE THR LEU ASN MET GLY SEQRES 4 F 179 VAL GLY GLU ALA ILE ALA ASP LYS LYS LEU LEU ASP ASN SEQRES 5 F 179 ALA ALA ALA ASP LEU ALA ALA ILE SER GLY GLN LYS PRO SEQRES 6 F 179 LEU ILE THR LYS ALA ARG LYS SER VAL ALA GLY PHE LYS SEQRES 7 F 179 ILE ARG GLN GLY TYR PRO ILE GLY CYS LYS VAL THR LEU SEQRES 8 F 179 ARG GLY GLU ARG MET TRP GLU PHE PHE GLU ARG LEU ILE SEQRES 9 F 179 THR ILE ALA VAL PRO ARG ILE ARG ASP PHE ARG GLY LEU SEQRES 10 F 179 SER ALA LYS SER PHE ASP GLY ARG GLY ASN TYR SER MET SEQRES 11 F 179 GLY VAL ARG GLU GLN ILE ILE PHE PRO GLU ILE ASP TYR SEQRES 12 F 179 ASP LYS VAL ASP ARG VAL ARG GLY LEU ASP ILE THR ILE SEQRES 13 F 179 THR THR THR ALA LYS SER ASP GLU GLU GLY ARG ALA LEU SEQRES 14 F 179 LEU ALA ALA PHE ASP PHE PRO PHE ARG LYS SEQRES 1 M 118 MET ALA ARG ILE ALA GLY ILE ASN ILE PRO ASP HIS LYS SEQRES 2 M 118 HIS ALA VAL ILE ALA LEU THR SER ILE TYR GLY VAL GLY SEQRES 3 M 118 LYS THR ARG SER LYS ALA ILE LEU ALA ALA ALA GLY ILE SEQRES 4 M 118 ALA GLU ASP VAL LYS ILE SER GLU LEU SER GLU GLY GLN SEQRES 5 M 118 ILE ASP THR LEU ARG ASP GLU VAL ALA LYS PHE VAL VAL SEQRES 6 M 118 GLU GLY ASP LEU ARG ARG GLU ILE SER MET SER ILE LYS SEQRES 7 M 118 ARG LEU MET ASP LEU GLY CYS TYR ARG GLY LEU ARG HIS SEQRES 8 M 118 ARG ARG GLY LEU PRO VAL ARG GLY GLN ARG THR LYS THR SEQRES 9 M 118 ASN ALA ARG THR ARG LYS GLY PRO ARG LYS PRO ILE LYS SEQRES 10 M 118 LYS CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000